AlignACE version 2.2 July 7, 1998 AlignACE -jSPS.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YDR522C 300 bp YDR522C SPS2 1-1509 Middle\/late gene of meiosis #2 YDR523C 503 bp YDR523C SPS1 1-1473 serine\/threonine kinase homologous to Ste20p\; expressed in middle\/late meiosis #3 YHR139C 600 bp YHR139C SPS100 1-981 sporulation-specific wall maturation protein #4 YNL204C_YNL202W 309 bp YNL204C SPS18 1-903 sporulation-specific protein YNL202W SPS19 1-888 peroxisomal 2,4-dienoyl-CoA reductase #5 YOR313C 300 bp YOR313C SPS4 1-1017 sporulation-specific protein Motif number 1 CACATTATATATATATATCTATTTTTTTAAACGAAT 1 39 0 ATTCTTTTTT 0.897734 -262 GTGTATATGCATGAGTTTTTGTTTTCCATTCTCTTT 1 74 1 ATTTTTTTTC 0.67325 -227 ATTTACCTGCTTATTTCTCCCTTTTTTTTTCGATTC 1 181 1 TTTCCTTTTT 0.974775 -120 TCCCTTTTTTTTTCGATTCTTTTTTTCTGATCGAGC 1 198 1 TTACTTTTTT 0.960213 -103 ATATGATAATTTAACTGTATTTTTTTCCCTTTTCTA 2 14 1 TTTATTTTTT 0.845742 -490 TTTTTTTCCCTTTTCTAATACTTTTTCCTCAAGTTA 2 33 1 TTTTATTTTT 0.931705 -471 TTTTTCGTTTTTATGTGTCATTTTTTTTTATCCCTG 2 107 0 TTTCATTTTT 0.960572 -397 AAGACACAAATTCCATTTTTTTTTTTTGACGCGAAA 2 141 1 TTTTTTTTTT 0.974978 -363 AAAGAGTCACTTAATATACTGTTTTTGTTTATTATC 2 249 1 TTACTTTTTT 0.960213 -255 AAGAAGAGAATTAGCTGGCTTTTTTTGGATAGGAAA 2 310 0 TTTCTTTTTT 0.985832 -194 AGCCAGCTAATTCTCTTCTTTTTTTTTCTTATTTTG 2 326 1 TTTTTTTTTT 0.974978 -178 TTTTTTTTTCTTATTTTGCCATTTTCAATATTATCG 2 344 1 TTTCCTTTTC 0.94185 -160 GCATTTGCTTTTTAAATTTAGTTTTTTTACTAGCTA 2 442 1 TTATATTTTT 0.825529 -62 CCCTTAACTGTTGAATGATCTTTTTCTGGTAGATCA 3 201 0 TTTTCTTTTC 0.900694 -400 TGTTTTTAGCTTTCCTCCCAATTTTTATAGTATTCT 3 491 0 TTTCATTTTT 0.960572 -110 TAAAAACACTTTTGGTTTCTCTTGTTCCTATCAATC 3 519 1 TTTCTTTGTT 0.931408 -82 ATATTAGAAATTACGAACTTCTTTTCAAATTTAGAT 4 237 0 TTATTTTTTC 0.84995 -73 CTCAAGAGGGTTTAGTATCCTTTTTTTGTTGGTTCC 5 38 1 TTTCCTTTTT 0.974775 -263 ACAAAATTTCTTCCTTTGTTATTTTTGAGAGGCAAG 5 214 1 TTTTTTTTTT 0.974978 -87 CAAAAACAATTTTTTATGTTCTTGTTGCTTGCCTCT 5 241 0 TTATTTTGTT 0.725067 -60 ** * ** ***** Masking position 12 Map Score: 23.3818 Number of sites scoring better than the average of aligned sites = 7575 Number in coding regions = 1770 Number in noncoding regions = 5805 Number of orfs with sites within 600 bp upstream = 1929 Fraction of orfs with sites within 600 bp upstream = 0.30983 Motif number 2 AAAATATTTTTTTTGAGACGCATCAATGAC 1 254 0 TTTTGAGACG 0.98666 -47 AAAAAAAATATTTTGTGGCATTACTTAGAC 1 270 1 TTTTGTGGCA 0.983616 -31 CATTTTTTTTTTTTGACGCGAAAGAATGAC 2 154 1 TTTTGACGCG 0.986823 -350 GTTTGCTTTCTTTTGAGAAATGTTTGCTAA 2 410 0 TTTTGAGAAA 0.895941 -94 CATCGGCTTCTTTTGACGCAGGAAAAGGCC 3 173 0 TTTTGACGCA 0.974436 -428 TTGAAAGTGATTTTGTGACGTTAGGCCAGC 4 108 0 TTTTGTGACG 0.983616 -202 AATGATACGTTTTTGTGGCGCGCGTCAATC 5 108 0 TTTTGTGGCG 0.991593 -193 AAGGAAGAAATTTTGTCGAAAGTGTAGTAG 5 200 0 TTTTGTCGAA 0.876185 -101 CCTTTGTTATTTTTGAGAGGCAAGCAACAA 5 226 1 TTTTGAGAGG 0.934295 -75 ********** Masking position 4 Map Score: 9.72843 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 325 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TAAACGAATCCTTTCTTTATTGCTTCAATTC 1 17 0 CTTTTTTATT 0.867406 -284 TATATCCATCCTTCATTTATTGAAGATGAAA 1 107 0 CTTCTTTATT 0.876561 -194 AACACATGACTTTTTACTGTTTGTTATATAA 1 143 0 TTTTACTGTT 0.788518 -158 AGTCATGTGTTTTTGATTATTTACCTGCTTA 1 163 1 TTTTATTATT 0.883958 -138 TTCTCCCTTTTTTTTTCGATTCTTTTTTTCT 1 195 1 TTTTTCGATT 0.770643 -106 TTTCTTTTATAGTCTAAGTAA 1 290 0 TTTCTTTATA 0.615711 -11 CAAATTCCATTTTTTTTTTTTGACGCGAAAG 2 147 1 TTTTTTTTTT 0.698369 -357 ATGACACTACTTTCTTCTATTGTAACCATTT 2 179 1 TTTCTCTATT 0.923841 -325 AACATCGATATTTTACTTGTTAGTTCAGATA 2 212 1 TTTTCTTGTT 0.920092 -292 AATATACTGTTTTTGTTTATTATCTTGGTTC 2 261 1 TTTTTTTATT 0.956057 -243 CTCTTCTTTTTTTTTCTTATTTTGCCATTTT 2 338 1 TTTTCTTATT 0.923563 -166 TATTTTGCCATTTTCAATATTATCGATTTAG 2 355 1 TTTTAATATT 0.654502 -149 TTTGTGCTATTTTCTTTTGTTGTTTAGTAAA 2 483 0 TTTCTTTGTT 0.957459 -21 TTGTACACGTTTTTCCCTATTTTCTGCTCAT 3 382 0 TTTTCCTATT 0.861225 -219 ACACTTTTGGTTTCTCTTGTTCCTATCAATC 3 524 1 TTTCCTTGTT 0.92592 -77 AAATTTAGATTTTCTTTGATTTGGAGCCTTA 4 216 0 TTTCTTGATT 0.876561 -94 AAGTTCGTAATTTCTAATATTTACACTTTTA 4 253 1 TTTCAATATT 0.672813 -57 AGTATCCTTTTTTTGTTGGTTCCTGCAGCAG 5 51 1 TTTTTTGGTT 0.861767 -250 GACAAAATTTCTTCCTTTGTTATTTTTGAGA 5 213 1 CTTCTTTGTT 0.871254 -88 GCAAAAACAATTTTTTATGTTCTTGTTGCTT 5 247 0 TTTTTATGTT 0.837561 -54 **** ****** Masking position 3 Map Score: 14.1205 Number of sites scoring better than the average of aligned sites = 5711 Number in coding regions = 2350 Number in noncoding regions = 3361 Number of orfs with sites within 600 bp upstream = 2001 Fraction of orfs with sites within 600 bp upstream = 0.321394 Motif number 4 AAAAAAAGAAGAGAATTAGCTGGCTTTTTT 2 321 0 GAGAATTAGC 0.887257 -183 CGCTTCCCTTGAAAATCGCCGAAAGAAGCT 3 127 1 GAAAATCGCC 0.905797 -474 TTTTCTGGTAGATCATCGGCTTCTTTTGAC 3 186 0 GATCATCGGC 0.982655 -415 ATTCGCTTCTGTACATCAGCCGGTATTCGC 3 252 0 GTACATCAGC 0.973131 -349 ATAAACCGAGGATCATCAGCGTTAAATGTA 3 354 0 GATCATCAGC 0.982925 -247 TGTATAATTTGTAAATTAGCGTTGTTTTTA 4 68 1 GTAAATTAGC 0.89314 -242 GTCAATCGGCGATAATCAGCAACGCGTCTG 5 85 0 GATAATCAGC 0.982217 -216 TGTGGCGCGCGTCAATCGGCGATAATCAGC 5 95 0 GTCAATCGGC 0.954391 -206 ********** Masking position 5 Map Score: 2.96057 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 318 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 TGAAGCAGTTGGAACCAAGATAATAAACAA 2 273 0 GGAACCAAGA 0.995535 -231 AGGAACAAGAGAAACCAAAAGTGTTTTTAG 3 518 0 GAAACCAAAA 0.914918 -83 GGTATAAAAGGGACCCAAGAATATATGGAC 4 21 0 GGACCCAAGA 0.995862 -289 TAAGACACAAGGACTCAAGAGGGTTTAGTA 5 25 1 GGACTCAAGA 0.978778 -276 CGCTGCTGCAGGAACCAACAAAAAAAGGAT 5 54 0 GGAACCAACA 0.98812 -247 ********** Masking position 7 Map Score: 2.81434 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 138 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TATCCAAAAAAAGCCAGCTAATTCTCTTCTT 2 315 1 AAGCAGCTAA 0.975854 -189 CATTTCTCAAAAGAAAGCAAACCAGCATTTG 2 418 1 AAGAAGCAAA 0.966416 -86 AAAATCGCCGAAAGAAGCTAAGCCGAAGTGA 3 138 1 AAAGAGCTAA 0.916841 -463 ATGTAATGTTAGAGTAGCAAAAGTTCTTGGC 3 315 1 AGAGAGCAAA 0.965581 -286 AAAAATTGGGAGGAAAGCTAAAAACACTTTT 3 501 1 AGGAAGCTAA 0.966046 -100 TTGTGACGTTAGGCCAGCAAACGCATAGTAA 4 95 0 AGGCAGCAAA 0.99037 -215 TATTTTTGAGAGGCAAGCAACAAGAACATAA 5 233 1 AGGCAGCAAC 0.964683 -68 ATGTGAAACCAATGTAGCAAAAACAATTTTT 5 263 0 AATGAGCAAA 0.90934 -38 **** ****** Masking position 6 Map Score: 2.82008 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 409 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 TCGAGCGTTTATGTCTTTACTGTCCCGTCA 1 228 1 ATGTCTTTAC 0.795575 -73 GGCTAGTCAGTTGTCTTAGCAAACATTTCT 2 395 1 TTGTCTTAGC 0.978191 -109 CCGTGTCACTTCGGCTTAGCTTCTTTCGGC 3 144 0 TCGGCTTAGC 0.930995 -457 GCAAAAGTTCTTGGCTTAGCAATTACATTT 3 331 1 TTGGCTTAGC 0.982977 -270 AAAAACACTTTTGGTTTCTCTTGTTCCTAT 3 520 1 TTGGTTTCTC 0.823608 -81 TAAATTAGCGTTGTTTTTACTATGCGTTTG 4 79 1 TTGTTTTTAC 0.917036 -231 TTGAGTCCTTGTGTCTTAACGACCGCATAG 5 13 0 GTGTCTTAAC 0.882501 -288 ACATAAAAAATTGTTTTTGCTACATTGGTT 5 258 1 TTGTTTTTGC 0.94604 -43 TTTTGCTACATTGGTTTCACATAACATATT 5 272 1 TTGGTTTCAC 0.938882 -29 ********** Masking position 6 Map Score: 0.94092 Number of sites scoring better than the average of aligned sites = 1227 Number in coding regions = 948 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 8 GATATGCACCCTTAAGGCGGACTTGATCTTC 3 66 0 CTTAAGGCGA 0.987762 -535 GCGTCTGCACCTTAACGCAGACAAATGACGC 3 99 0 CTTAACGCGA 0.996494 -502 AGCAATTACATTTAACGCTGATGATCCTCGG 3 348 1 TTTAACGCGA 0.986213 -253 GTTTGATATACTTAACGCCGTGAGTGTACGC 4 143 0 CTTAACGCGT 0.988556 -167 CGCGTTGCTGATTATCGCCGATTGACGCGCG 5 89 1 ATTATCGCGA 0.956028 -212 ******** ** Masking position 4 Map Score: 1.62466 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 21 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 GCTTATTTCTCCCTTTTTTTTTCGATTCTT 1 189 1 CCCTTTTTTT 0.916155 -112 GTATTTTTTTCCCTTTTCTAATACTTTTTC 2 30 1 CCCTTTTCTA 0.981578 -474 AACTAGCATCCCCTTTTAGAAATGCCTTGT 3 433 1 CCCTTTTAGA 0.989905 -168 ATTCTTGGGTCCCTTTTATACCAGTACTCT 4 29 1 CCCTTTTATA 0.989111 -281 CTAATATTTACACTTTTAGAGTTTGGGAGG 4 266 1 CACTTTTAGA 0.949469 -44 ********** Masking position 5 Map Score: 0.702369 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 155 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 10 ********** No masking Map Score: 4.50017e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 4.50017e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ATAATCAAAAACACATGACTTTTTACTGTT 1 153 0 ACACATGACT 0.978584 -148 TTTGAGACGCATCAATGACGGGACAGTAAA 1 243 0 ATCAATGACG 0.915849 -58 ATTTTTTTTTATCCCTGATGCCGCATTGTT 2 94 0 ATCCCTGATG 0.794668 -410 GATTTAGTGAACACCTGGCTAGTCAGTTGT 2 379 1 ACACCTGGCT 0.922809 -125 GTTTGCTAAGACAACTGACTAGCCAGGTGT 2 389 0 ACAACTGACT 0.965993 -115 CTTAACGCAGACAAATGACGCATGATATGC 3 90 0 ACAAATGACG 0.965993 -511 AAAAACGTGTACAAATGATTCTCTCAGAAT 3 399 1 ACAAATGATT 0.868912 -202 AGTATCCATGACTCGAACATACG 4 297 0 ATCCATGACT 0.945515 -13 ********** Masking position 1 Map Score: 0.153246 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 507 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 13 ********** No masking Map Score: 4.50017e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 4.50017e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 4.50017e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0